Formal Cellular Machinery

https://doi.org/10.1016/j.entcs.2012.05.015Get rights and content
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Abstract

Various calculi have been proposed to model different levels of abstraction of cell signaling and molecular interactions. In this paper we propose a framework inspired by some of these calculi that structures interactions and agents from the most basic elements of the cell (protein interaction sites) to higher order ones (compartments and molecular species).

Keywords

systems biology
compartment
rule-based modeling
kappa
bigraphs
projectivity
membrane
term rewriting

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